Use `pak` when package installation is not found #284

schloerke · 2021-03-18T18:47:58Z

Fixes #234

This PR is to get the conversation going to hopefully remove maintenance requirements of shinyapps.io by offloading to pak which uses RSPM to query rstudio/r-system-requirements

Benefits:

Unify the installation patterns
Stop playing wack-a-mole on installations failures that are defined elsewhere
From https://github.com/rstudio/r-system-requirements readme:

This metric indicates how good the rules are for the majority of packages R users are likely to install
Ubuntu 18
No rules 90.1%
With rules 99.2%".

Setup:

If there is no install script, then pak is used.
- This PR does not use the CRAN version of pak. Instead, it uses the hosted version provided by RStudio's r-lib team. This is done to update rapidly as bug fixes are found. I'd recommend moving to a CRAN installation once the dev version makes it to CRAN.
- Disadvantage: This requires RSPM to work / function, whereas the static files are known at install time.
If there is a package install script, the install script is used.
- Using the existing install script will not install dependencies for the required packages. I do not know which packages are supplied at install time. Ex: rgl originally only wanted to install libgl1-mesa-dev and libgl-mesa-dev, where pak says it requires:

❯❯ pak::pkg_system_requirements("rgl", "ubuntu", "18.04")
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

Alterations:

I have removed simple installation files that immediately matched ubuntu 18.04. If there were more complicated ones, like sodium, I did not remove their install script.
I am working on making a GitHub Action to test all known packages. (bionic && xenial)

Future:

Game plan moving forward. I'd recommend spamming the few handful of authors for packages like av which require system installations, but do not report them so that rstudio/r-system-requirements picks them up automatically. (Curious as to why av by Jeroen doesn't have any pak sys reqs when its SystemRequirements looks like: FFmpeg (>= 3.2); with at least libx264 and lame (mp3) drivers. Debian/Ubuntu:libavfilter-dev, Fedora/CentOS: ffmpeg-devel (via https://rpmfusion.org), MacOS Homebrew: ffmpeg.)

`pak` system requirements for existing packages

ubuntu 16.04 sys requirements

❯❯ pkgs %>% setNames(., .)%>% lapply(pak::pkg_system_requirements, "ubuntu", "16.04")
$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y swftools"
[5] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:cran/libgit2"
[3] "apt-get update"                                "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"                 "apt-get install -y git"
[7] "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
character(0)

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgeos-dev"
[5] "apt-get install -y libproj-dev"                "apt-get install -y libgdal-dev"
[7] "apt-get install -y gdal-bin"                   "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:ubuntugis/ppa"
[3] "apt-get update"                                "apt-get install -y libgdal-dev"
[5] "apt-get install -y gdal-bin"                   "apt-get install -y libgeos-dev"
[7] "apt-get install -y libproj-dev"                "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

ubuntu 18.04 sys requirements

$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y swftools"
[5] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y software-properties-common" "add-apt-repository -y ppa:cran/libgit2"
[3] "apt-get update"                                "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"                 "apt-get install -y git"
[7] "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
[1] "apt-get install -y libjq-dev"

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y libgeos-dev"     "apt-get install -y libproj-dev"     "apt-get install -y libgdal-dev"
[4] "apt-get install -y gdal-bin"        "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y libgdal-dev"     "apt-get install -y gdal-bin"        "apt-get install -y libgeos-dev"
[4] "apt-get install -y libproj-dev"     "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

ubuntu 20.04 sys requirements

$animation
[1] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"
[3] "apt-get install -y texlive"              "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"

$av
character(0)

$convertGraph
character(0)

$docxtractr
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$gdalUtils
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$gert
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libgit2-dev"

$gmp
[1] "apt-get install -y libgmp3-dev"

$gridGraphics
character(0)

$gsl
[1] "apt-get install -y libgsl0-dev"

$hunspell
character(0)

$igraph
[1] "apt-get install -y libglpk-dev" "apt-get install -y libgmp3-dev" "apt-get install -y libxml2-dev"

$jqr
[1] "apt-get install -y libjq-dev"

$keyring
[1] "apt-get install -y libsodium-dev"   "apt-get install -y libsecret-1-dev" "apt-get install -y libssl-dev"

$lwgeom
[1] "apt-get install -y libgeos-dev"     "apt-get install -y libproj-dev"     "apt-get install -y libgdal-dev"
[4] "apt-get install -y gdal-bin"        "apt-get install -y libudunits2-dev"

$magick
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y imagemagick"          "apt-get install -y libmagick++-dev"

$ncdf4
[1] "apt-get install -y libnetcdf-dev"

$openbabel
character(0)

$pagedown
[1] "apt-get install -y libicu-dev" "apt-get install -y pandoc"     "apt-get install -y make"
[4] "apt-get install -y libssl-dev"

$pdftools
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libpoppler-cpp-dev"

$pensieve
character(0)

$ragg
[1] "apt-get install -y libfontconfig1-dev" "apt-get install -y libfreetype6-dev"
[3] "apt-get install -y libjpeg-dev"        "apt-get install -y libpng-dev"
[5] "apt-get install -y libtiff-dev"        "apt-get install -y libfribidi-dev"
[7] "apt-get install -y libharfbuzz-dev"

$RAmazonS3
character(0)

$rcbc
character(0)

$rcdd
[1] "apt-get install -y libgmp3-dev"

$rDEA
[1] "apt-get install -y libglpk-dev"

$redland
[1] "apt-get install -y libxml2-dev" "apt-get install -y libicu-dev"  "apt-get install -y librdf0-dev"
[4] "apt-get install -y pandoc"

$rgdal
[1] "apt-get install -y libgdal-dev" "apt-get install -y gdal-bin"    "apt-get install -y libproj-dev"

$rgeos
[1] "apt-get install -y libgeos-dev"

$rgl
 [1] "apt-get install -y imagemagick"      "apt-get install -y libmagick++-dev"  "apt-get install -y make"
 [4] "apt-get install -y libicu-dev"       "apt-get install -y pandoc"           "apt-get install -y libfreetype6-dev"
 [7] "apt-get install -y libglu1-mesa-dev" "apt-get install -y libpng-dev"       "apt-get install -y libgl1-mesa-dev"
[10] "apt-get install -y zlib1g-dev"

$Rglpk
[1] "apt-get install -y libglpk-dev"

$rJava
[1] "apt-get install -y make"        "apt-get install -y default-jdk"

$Rmpfr
[1] "apt-get install -y libgmp3-dev" "apt-get install -y libmpfr-dev"

$Rpoppler
[1] "apt-get install -y libglib2.0-dev"     "apt-get install -y libpoppler-cpp-dev"

$rPython
character(0)

$RSelenium
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libxml2-dev"

$rsvg
[1] "apt-get install -y librsvg2-dev"

$Rsymphony
character(0)

$seewave
[1] "apt-get install -y libsndfile1-dev"

$sf
[1] "apt-get install -y libgdal-dev"     "apt-get install -y gdal-bin"        "apt-get install -y libgeos-dev"
[4] "apt-get install -y libproj-dev"     "apt-get install -y libudunits2-dev"

$sodium
[1] "apt-get install -y libsodium-dev"

$ssh
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y git"                  "apt-get install -y libssh2-1-dev"

$staplr
[1] "apt-get install -y make"        "apt-get install -y default-jdk" "apt-get install -y libxml2-dev"
[4] "apt-get install -y libicu-dev"

$tensorflow
[1] "apt-get install -y python"

$tesseract
[1] "apt-get install -y libleptonica-dev"     "apt-get install -y libtesseract-dev"
[3] "apt-get install -y tesseract-ocr-eng"    "apt-get install -y libcurl4-openssl-dev"
[5] "apt-get install -y libssl-dev"           "apt-get install -y libpoppler-cpp-dev"

$tiff
[1] "apt-get install -y libjpeg-dev" "apt-get install -y libtiff-dev"

$tkrplot
character(0)

$tm
[1] "apt-get install -y libxml2-dev"

$topicmodels
[1] "apt-get install -y libxml2-dev" "apt-get install -y libgsl0-dev"

$udunits2
[1] "apt-get install -y libudunits2-dev"

$units
[1] "apt-get install -y libudunits2-dev"

$V8
[1] "apt-get install -y libcurl4-openssl-dev" "apt-get install -y libssl-dev"
[3] "apt-get install -y libv8-dev"

$websocket
[1] "apt-get install -y make"       "apt-get install -y libssl-dev"

$xslt
[1] "apt-get install -y libxml2-dev" "apt-get install -y libxslt-dev"

GitHub Actions Testing

Testing all packages on focal and xenial. Packages that have an install file will use it, otherwise pak will be used.

https://github.com/schloerke/shinyapps-package-dependencies/runs/2143004651?check_suite_focus=true

cc @samperman

…stall sys reqs

* master: Standardize on OS_CODENAME instead of OS_DISTRIBUTION update the CHANGELOG.md to reflect removed packages our base images no longer need extra things installed for rPython to work. neither focal nor xenial need this installed for this package to work remove vivid/trusty/precise, only worry about xenial and focal PR feedback rcbc has some different install requirements, and also needs -y in the install step. It was never actually doing anything fix openbabel for focal, requires libeigen3-dev, which is a source package only on focal... python-software-properties doesn't exist in focal it seems do not support docxtractr on focal on travis this is prompting for user input, make sure it doesn't hopeful changelog updates add focal Dockerfile, and change Makefile to have focal tests instead of bionic still not working for focal update packages to support focal Update CHANGELOG.md add support for focal to animation add focal dockerfile and update the makefile to support it. Remove bionic.

schloerke added 30 commits March 18, 2021 10:28

Setup pak

7b933ef

Use local lib path for pak that is ignored for regular execution

93362ed

Fix pkgs to be installed

0114221

Install pak before packages. If no install file exists, use pak to in…

fdf66eb

…stall sys reqs

Ignore lib folder

bb51c28

Remove gsl install

5d590b2

remove pdftools install

c722231

remove ragg install

4adbd13

remove rDEA install and test

727e2ca

remove redland install

e9eae2d

remove rgeos install

0f30a34

remove rgl

2190bfa

remove Rglpk

066f585

remove Rmpfr install

8e9d0e3

remove rsvg install

18fa843

remove tesseract

02ea033

remove textshaping

c5864a7

Remove tiff

3314d33

remove units and udunits2

e922be7

remove V8 install

d56ca26

Rename pak install pkg file

62018f8

Create test-pkgs.yaml

fdc6291

Don't forget to checkout the repo. Run on pak branch

09bf627

try using an object and no an array

8499d49

Use a matrix like the example

28c3722

Revert to original single name setup. Say test needs packages

79d5525

Use hosted docker images

8fcb11a

formatting

3bd9e30

Test using focal

e2dc63e

schloerke added 2 commits March 18, 2021 15:21

Delete .travis.yml

a903ac8

xenial is missing libpcre2. Build local docker files to test latest

c39737d

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Use `pak` when package installation is not found #284

Use `pak` when package installation is not found #284

schloerke commented Mar 18, 2021 •

edited

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Use pak when package installation is not found #284

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Use pak when package installation is not found #284

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schloerke commented Mar 18, 2021 • edited Loading

Benefits:

Setup:

Alterations:

Future:

pak system requirements for existing packages

GitHub Actions Testing

Use `pak` when package installation is not found #284

Use `pak` when package installation is not found #284

schloerke commented Mar 18, 2021 •

edited

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`pak` system requirements for existing packages